Melatonin is the main hormone of seasonal breeding in sheep and goat which has an effect on reproductive organs via its receptors. Studies have shown that mutations in melatonin receptor 1A ( MTNR 1A) gene are related to litter size as well as the ovulation rate in sheep and goats. In this study, polymorphism of two loci in MTNR 1A melatonin receptor gene was studied in order to survey their relationship with litter size in Markhoz goats. PCR primers were employed to mask polymorphisms of MTNR 1A in 150 does by PCR ‐ RFLP method. After DNA extraction, the PCR ‐ RFLP was performed using Ecol31 I and Hpa I restriction enzymes. Results showed that these loci were not polymorphic. These results show that the fecundity of Markhoz goats is not linked to MTNR 1A. No polymorphism in MTNR 1A was found in Markhoz goats, therefore, it is essential to test polymorphism of other genes or loci to facilitate marker‐assisted selection techniques to improve reproduction traits in Markhoz goats.